Knotting dynamics of DNA chains of different length confined in nanochannels
Knotting dynamics of DNA chains of different length confined in nanochannels
复制标题
纳米通道内不同长度DNA链的打结动力学
DOI：
--
复制
发表时间：
2015
期刊：
影响因子：
--
通讯作者：
C. Micheletti
中科院分区：
文献类型：
--
作者：
A. Suma;E. Orlandini;C. Micheletti
Langevin动力学模拟被用来表征的典型机制的自发捆绑，解开和结的动力学演化的粗粒度模型的DNA链被限制在纳米通道。特别是，我们专注于这些机制如何依赖于链轮廓长度，LC，在一个固定的通道宽度D = 56 nm对应的Odijk缩放制度的发病链回折，因此结是不利的，但不完全抑制。我们发现，结的寿命显着增长与Lc，而unknots变化较小的程度。基本的动力学机制澄清通过分析的节点位置的演变沿着链。事实上，在所考虑的约束条件下，结通常是由链末端的局部后折所系结的，在链末端，结在沿链沿着随机运动后最终解结。因此，解开的寿命主要由链端的回折事件控制，这在很大程度上独立于Lc。相反，结的寿命随着Lc而显著增加，因为结在解开之前平均可以沿着链行进沿着更远。观察到的相互作用的结和解结寿命的基础增长的平衡打结的概率越来越长的链在固定的通道限制。
Langevin dynamics simulations are used to characterize the typical mechanisms governing the spontaneous tying, untying and the dynamical evolution of knots in coarse-grained models of DNA chains confined in nanochannels. In particular we focus on how these mechanisms depend on the chain contour length, Lc, at a fixed channel width D = 56 nm corresponding to the onset of the Odijk scaling regime where chain backfoldings and hence knots are disfavoured but not suppressed altogether. We find that the lifetime of knots grows significantly with Lc, while that of unknots varies to a lesser extent. The underlying kinetic mechanisms are clarified by analysing the evolution of the knot position along the chain. At the considered confinement, in fact, knots are typically tied by local backfoldings of the chain termini where they are eventually untied after a stochastic motion along the chain. Consequently, the lifetime of unknots is mostly controlled by backfoldings events at the chain ends, which is largely independent of Lc. The lifetime of knots, instead, increases significantly with Lc because knots can, on average, travel farther along the chain before being untied. The observed interplay of knots and unknots lifetimes underpins the growth of the equilibrium knotting probability of longer and longer chains at fixed channel confinement.
登录
查看更多内容
影响因子：
10.8
作者：
Levy SL;Mannion JT;Cheng J;Reccius CH;Craighead HG
通讯作者：
Craighead HG
沿着拉伸 DNA 分子的结扩散的布朗动力学模拟。
DOI：
10.1529/biophysj.105.074682
发表时间：
2006
期刊：
Biophysical journal.
影响因子：
--
作者：
Vologodskii,Alexander
通讯作者：
Vologodskii,Alexander
限制在纳米通道中的半柔性聚合物的链刚度和排除体积之间的相互作用
影响因子：
4.4
作者：
Muralidhar, Abhiram;Tree, Douglas R.;Dorfman, Kevin D.
通讯作者：
Dorfman, Kevin D.
影响因子：
62.1
作者：
Dorfman, Kevin D.;King, Scott B.;Olson, Daniel W.;Thomas, Joel D. P.;Tree, Douglas R.
通讯作者：
Tree, Douglas R.
DOI：
--
发表时间：
2004
影响因子：
11.1
作者：
J. Tegenfeldt;C. Prinz;H. Cao;S. Chou;W. Reisner;R. Riehn;Yan Mei Wang;E. Cox;J. Sturm;
通讯作者：
J. Tegenfeldt;C. Prinz;H. Cao;S. Chou;W. Reisner;R. Riehn;Yan Mei Wang;E. Cox;J. Sturm;